Error: FileNotFoundError: Surfrecon missing: pial-lh-reordered.vtp

[dnkennedy]

What happened?

This is very similar to #444 I believe, but different.

I ran:

  nibabies-wrapper docker /Users/kennedyd/Data/Sohye/Infants/CHBabies/BB036_01/BIDS /Users/kennedyd/Data/Sohye/Infants/nibabies7 participant -i nipreps/nibabies:25.0.0 --participant-label BB03601 --fs-license-file /Users/kennedyd/license.txt --cifti-output --resource-monitor --stop-on-first-crash -w /Volumes/UMA2T/tmp2 --derivatives  smriprep=/Users/kennedyd/Data/Sohye/Infants/CHBabies/BB036_01/bibsanat --ignore fieldmaps --surface-recon-method mcribs --output-spaces MNIInfant:cohort-3:res-2

On Mac (Sonoma 14.5), using Docker (Engine: 27.4.0).

My smriprep is from BIBSNet, and using the surface-recon-method mcribs.

I get an error (will put the gory details below):

Running command:
MCRIBSurfReconDeformable sub-BB03601_ses-1 1.0 True False False
Stderr:

Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 404, in run
outputs = self.aggregate_outputs(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 433, in aggregate_outputs
predicted_outputs = self._list_outputs() # Predictions from _list_outputs
^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/mcribs.py", line 252, in _list_outputs
self._verify_outputs('surfrecon', surfrecon_dir, error=True)
File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/mcribs.py", line 289, in _verify_outputs
raise FileNotFoundError(f'{step.capitalize()} missing: {fl}')
FileNotFoundError: Surfrecon missing: pial-lh-reordered.vtp

What command did you use?

>  nibabies-wrapper docker /Users/kennedyd/Data/Sohye/Infants/CHBabies/BB036_01/BIDS /Users/kennedyd/Data/Sohye/Infants/nibabies7 participant -i nipreps/nibabies:25.0.0 --participant-label BB03601 --fs-license-file /Users/kennedyd/license.txt --cifti-output --resource-monitor --stop-on-first-crash -w /Volumes/UMA2T/tmp2 --derivatives  smriprep=/Users/kennedyd/Data/Sohye/Infants/CHBabies/BB036_01/bibsanat --ignore fieldmaps --surface-recon-method mcribs --output-spaces MNIInfant:cohort-3:res-2

What version of NiBabies are you using?

nibabies:25.0.0

Relevant log output

Running nibabies version 25.0.0:
      * BIDS dataset path: /data.
      * Participant list: [['BB03601', '1']].
      * Run identifier: 20250130-210125_0a746234-9b16-4376-8484-8e6225c504b0.
      * Output spaces: MNIInfant:cohort-3:res-2.
      * Derivatives: {'smriprep': PosixPath('/deriv/smriprep')}.
      * Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-3/tpl-MNIInfant_cohort-3_res-1_T1w.nii.gz
100%|██████████████████████████████████████| 11.6M/11.6M [00:02<00:00, 5.41MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-3/tpl-MNIInfant_cohort-3_res-1_desc-brain_mask.nii.gz
100%|████████████████████████████████████████| 114k/114k [00:00<00:00, 1.99MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-3/tpl-MNIInfant_cohort-3_res-1_T2w.nii.gz
100%|██████████████████████████████████████| 11.7M/11.7M [00:04<00:00, 2.35MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-4/tpl-MNIInfant_cohort-4_res-1_T1w.nii.gz
100%|██████████████████████████████████████| 11.9M/11.9M [00:03<00:00, 3.05MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-4/tpl-MNIInfant_cohort-4_res-1_desc-brain_mask.nii.gz
100%|████████████████████████████████████████| 115k/115k [00:00<00:00, 1.98MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-4/tpl-MNIInfant_cohort-4_res-1_T2w.nii.gz
100%|██████████████████████████████████████| 11.8M/11.8M [00:05<00:00, 2.09MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-3/tpl-MNIInfant_cohort-3_res-2_desc-brain_mask.nii.gz
100%|██████████████████████████████████████| 19.9k/19.9k [00:00<00:00, 4.49MB/s]
250130-21:02:26,952 nipype.workflow IMPORTANT:
	 nibabies started!
250130-21:03:12,111 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bidssrc" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bidssrc".
250130-21:03:13,74 nipype.workflow INFO:
	 [Node] Executing "bidssrc" <niworkflows.interfaces.bids.BIDSDataGrabber>
250130-21:03:13,76 nipype.interface INFO:
	 No "flair" images found for sub-BB03601
250130-21:03:13,76 nipype.interface INFO:
	 No "sbref" images found for sub-BB03601
250130-21:03:13,77 nipype.interface INFO:
	 No "roi" images found for sub-BB03601
250130-21:03:13,77 nipype.interface INFO:
	 No "pet" images found for sub-BB03601
250130-21:03:13,77 nipype.interface INFO:
	 No "asl" images found for sub-BB03601
250130-21:03:13,78 nipype.workflow INFO:
	 [Node] Finished "bidssrc", elapsed time 0.001587s.
250130-21:03:16,46 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.infant_anat_fit_wf.coregistration_wf.reg_mask" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/infant_anat_fit_wf/coregistration_wf/reg_mask".
250130-21:03:17,87 nipype.workflow INFO:
	 [Node] Executing "reg_mask" <niworkflows.interfaces.nibabel.BinaryDilation>
250130-21:04:38,553 nipype.workflow INFO:
	 [Node] Finished "reg_mask", elapsed time 81.465268s.
250130-21:04:40,418 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.infant_anat_fit_wf.coregistration_wf.refine_mask" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/infant_anat_fit_wf/coregistration_wf/refine_mask".
250130-21:04:41,181 nipype.workflow INFO:
	 [Node] Executing "refine_mask" <niworkflows.interfaces.nibabel.BinaryDilation>
250130-21:05:54,955 nipype.workflow INFO:
	 [Node] Finished "refine_mask", elapsed time 73.773514s.
250130-21:05:56,544 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.infant_anat_fit_wf.segmentation_wf.to_dseg" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/infant_anat_fit_wf/segmentation_wf/to_dseg".
250130-21:05:57,952 nipype.workflow INFO:
	 [Node] Executing "to_dseg" <nipype.interfaces.utility.wrappers.Function>
250130-21:05:58,830 nipype.workflow INFO:
	 [Node] Finished "to_dseg", elapsed time 0.877321s.
250130-21:06:00,469 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.fs_to_mcribs" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/infant_anat_fit_wf/mcribs_surface_recon_wf/fs_to_mcribs".
250130-21:06:00,665 nipype.workflow INFO:
	 [Node] Executing "fs_to_mcribs" <niworkflows.interfaces.nibabel.MapLabels>
250130-21:06:02,217 nipype.workflow INFO:
	 [Node] Finished "fs_to_mcribs", elapsed time 1.551485s.
250130-21:06:04,448 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.infant_anat_fit_wf.mcribs_surface_recon_wf.mask_dil" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/infant_anat_fit_wf/mcribs_surface_recon_wf/mask_dil".
250130-21:06:04,678 nipype.workflow INFO:
	 [Node] Executing "mask_dil" <niworkflows.interfaces.morphology.BinaryDilation>
250130-21:06:11,891 nipype.workflow INFO:
	 [Node] Finished "mask_dil", elapsed time 7.212764s.
250130-21:06:14,412 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_fit_wf.hmc_boldref_wf.val_bold" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_fit_wf/hmc_boldref_wf/val_bold".
250130-21:06:14,838 nipype.workflow INFO:
	 [Node] Executing "val_bold" <niworkflows.interfaces.header.ValidateImage>
250130-21:06:25,506 nipype.workflow INFO:
	 [Node] Finished "val_bold", elapsed time 10.666162s.
250130-21:06:26,432 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_fit_wf.hmc_boldref_wf.get_dummy" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_fit_wf/hmc_boldref_wf/get_dummy".
250130-21:06:26,648 nipype.workflow INFO:
	 [Node] Executing "get_dummy" <niworkflows.interfaces.bold.NonsteadyStatesDetector>
250130-21:06:29,207 nipype.workflow INFO:
	 [Node] Finished "get_dummy", elapsed time 2.558s.
250130-21:06:30,417 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_fit_wf.ds_hmc_boldref_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_fit_wf/ds_hmc_boldref_wf/sources".
250130-21:06:30,674 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:06:30,675 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000702s.
250130-21:06:32,442 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_fit_wf.ds_hmc_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_fit_wf/ds_hmc_wf/sources".
250130-21:06:32,749 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:06:32,750 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000252s.
250130-21:06:34,430 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_native_wf.bold_source" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_native_wf/bold_source".
250130-21:06:34,716 nipype.workflow INFO:
	 [Node] Executing "bold_source" <nipype.interfaces.utility.base.Select>
250130-21:06:34,720 nipype.workflow INFO:
	 [Node] Finished "bold_source", elapsed time 0.001201s.
250130-21:06:36,405 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.subcortical_mni_alignment_wf.atlas_rois" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/subcortical_mni_alignment_wf/atlas_rois".
250130-21:06:36,587 nipype.workflow INFO:
	 [Node] Executing "atlas_rois" <nibabies.interfaces.workbench.VolumeAllLabelsToROIs>
250130-21:06:37,377 nipype.workflow INFO:
	 [Node] Finished "atlas_rois", elapsed time 0.596796s.
250130-21:06:38,462 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.subcortical_mni_alignment_wf.atlas_labels" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/subcortical_mni_alignment_wf/atlas_labels".
250130-21:06:38,682 nipype.workflow INFO:
	 [Node] Executing "atlas_labels" <nibabies.interfaces.workbench.VolumeLabelExportTable>
250130-21:06:39,37 nipype.workflow INFO:
	 [Node] Finished "atlas_labels", elapsed time 0.261931s.
250130-21:06:40,434 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_grayords_wf.reorient_labels" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_grayords_wf/reorient_labels".
250130-21:06:40,685 nipype.workflow INFO:
	 [Node] Executing "reorient_labels" <nibabies.interfaces.nibabel.ReorientImage>
250130-21:06:40,722 nipype.workflow INFO:
	 [Node] Finished "reorient_labels", elapsed time 0.036613s.
250130-21:06:42,455 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_02_wf.bold_grayords_wf.gen_cifti_metadata" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_02_wf/bold_grayords_wf/gen_cifti_metadata".
250130-21:06:42,634 nipype.workflow INFO:
	 [Node] Executing "gen_cifti_metadata" <nipype.interfaces.utility.wrappers.Function>
250130-21:06:43,361 nipype.workflow INFO:
	 [Node] Finished "gen_cifti_metadata", elapsed time 0.726512s.
250130-21:06:44,412 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_fit_wf.hmc_boldref_wf.val_bold" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_fit_wf/hmc_boldref_wf/val_bold".
250130-21:06:44,690 nipype.workflow INFO:
	 [Node] Executing "val_bold" <niworkflows.interfaces.header.ValidateImage>
250130-21:06:54,471 nipype.workflow INFO:
	 [Node] Finished "val_bold", elapsed time 9.779522s.
250130-21:06:56,368 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_fit_wf.hmc_boldref_wf.get_dummy" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_fit_wf/hmc_boldref_wf/get_dummy".
250130-21:06:56,557 nipype.workflow INFO:
	 [Node] Executing "get_dummy" <niworkflows.interfaces.bold.NonsteadyStatesDetector>
250130-21:06:58,592 nipype.workflow INFO:
	 [Node] Finished "get_dummy", elapsed time 2.035298s.
250130-21:07:00,493 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_fit_wf.ds_hmc_boldref_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_fit_wf/ds_hmc_boldref_wf/sources".
250130-21:07:00,733 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:07:00,735 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000195s.
250130-21:07:02,402 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_fit_wf.ds_hmc_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_fit_wf/ds_hmc_wf/sources".
250130-21:07:02,579 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:07:02,580 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000193s.
250130-21:07:04,391 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_native_wf.bold_source" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_native_wf/bold_source".
250130-21:07:04,663 nipype.workflow INFO:
	 [Node] Executing "bold_source" <nipype.interfaces.utility.base.Select>
250130-21:07:04,664 nipype.workflow INFO:
	 [Node] Finished "bold_source", elapsed time 0.000294s.
250130-21:07:06,369 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.subcortical_mni_alignment_wf.atlas_rois" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/subcortical_mni_alignment_wf/atlas_rois".
250130-21:07:06,720 nipype.workflow INFO:
	 [Node] Executing "atlas_rois" <nibabies.interfaces.workbench.VolumeAllLabelsToROIs>
250130-21:07:07,399 nipype.workflow INFO:
	 [Node] Finished "atlas_rois", elapsed time 0.58048s.
250130-21:07:08,358 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.subcortical_mni_alignment_wf.atlas_labels" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/subcortical_mni_alignment_wf/atlas_labels".
250130-21:07:08,611 nipype.workflow INFO:
	 [Node] Executing "atlas_labels" <nibabies.interfaces.workbench.VolumeLabelExportTable>
250130-21:07:09,103 nipype.workflow INFO:
	 [Node] Finished "atlas_labels", elapsed time 0.395371s.
250130-21:07:10,368 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_grayords_wf.reorient_labels" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_grayords_wf/reorient_labels".
250130-21:07:10,658 nipype.workflow INFO:
	 [Node] Executing "reorient_labels" <nibabies.interfaces.nibabel.ReorientImage>
250130-21:07:10,757 nipype.workflow INFO:
	 [Node] Finished "reorient_labels", elapsed time 0.098711s.
250130-21:07:12,362 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_08_wf.bold_grayords_wf.gen_cifti_metadata" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_08_wf/bold_grayords_wf/gen_cifti_metadata".
250130-21:07:12,615 nipype.workflow INFO:
	 [Node] Executing "gen_cifti_metadata" <nipype.interfaces.utility.wrappers.Function>
250130-21:07:12,697 nipype.workflow INFO:
	 [Node] Finished "gen_cifti_metadata", elapsed time 0.081505s.
250130-21:07:14,353 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_09_wf.bold_fit_wf.hmc_boldref_wf.val_bold" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_09_wf/bold_fit_wf/hmc_boldref_wf/val_bold".
250130-21:07:14,613 nipype.workflow INFO:
	 [Node] Executing "val_bold" <niworkflows.interfaces.header.ValidateImage>
250130-21:07:25,682 nipype.workflow INFO:
	 [Node] Finished "val_bold", elapsed time 11.068667s.
250130-21:07:26,406 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_09_wf.bold_fit_wf.hmc_boldref_wf.get_dummy" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_09_wf/bold_fit_wf/hmc_boldref_wf/get_dummy".
250130-21:07:26,581 nipype.workflow INFO:
	 [Node] Executing "get_dummy" <niworkflows.interfaces.bold.NonsteadyStatesDetector>
250130-21:07:28,965 nipype.workflow INFO:
	 [Node] Finished "get_dummy", elapsed time 2.383367s.
250130-21:07:30,406 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_09_wf.bold_fit_wf.ds_hmc_boldref_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_09_wf/bold_fit_wf/ds_hmc_boldref_wf/sources".
250130-21:07:30,606 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:07:30,607 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000242s.
250130-21:07:32,434 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_09_wf.bold_fit_wf.ds_hmc_wf.sources" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_09_wf/bold_fit_wf/ds_hmc_wf/sources".
250130-21:07:32,670 nipype.workflow INFO:
	 [Node] Executing "sources" <nibabies.interfaces.bids.BIDSURI>
250130-21:07:32,671 nipype.workflow INFO:
	 [Node] Finished "sources", elapsed time 0.000408s.
250130-21:07:34,374 nipype.workflow INFO:
	 [Node] Setting-up "nibabies_25_0_wf.single_subject_sub-BB03601_ses-1_wf.bold_ses_1_task_rest_run_09_wf.bold_native_wf.bold_source" in "/scratch/nibabies_25_0_wf/single_subject_sub-BB03601_ses-1_wf/bold_ses_1_task_rest_run_09_wf/bold_native_wf/bold_source".
250130-21:07:34,744 nipype.workflow INFO:
	 [Node] Executing "bold_source" <nipype.interfaces.utility.base.Select>

...
	Running command:
		MCRIBSurfReconDeformable sub-BB03601_ses-1 1.0 True False False
Stderr:

Traceback:
	Traceback (most recent call last):
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 404, in run
	    outputs = self.aggregate_outputs(runtime)
	              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nipype/interfaces/base/core.py", line 433, in aggregate_outputs
	    predicted_outputs = self._list_outputs()  # Predictions from _list_outputs
	                        ^^^^^^^^^^^^^^^^^^^^
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/mcribs.py", line 252, in _list_outputs
	    self._verify_outputs('surfrecon', surfrecon_dir, error=True)
	  File "/opt/conda/envs/nibabies/lib/python3.11/site-packages/nibabies/interfaces/mcribs.py", line 289, in _verify_outputs
	    raise FileNotFoundError(f'{step.capitalize()} missing: {fl}')
	FileNotFoundError: Surfrecon missing: pial-lh-reordered.vtp

Add any additional information or context about the problem here.

I think my BIBSNet segmentations look ok.

[mgxd]

Is this a regression for something that was previously working, or first time try with this subject / segmentation? Unfortunately that error is quite broad, but generally boils down to something being not quite right within the segmentation (MCRIBS can be quite finicky at times, and even manual segmentations have been seen to fail). I've been meaning to work with a colleague who is an expert to put together a little FAQ of common gotchas.

Just curious - have you tried running with infantfs instead, still leveraging the segmentations? After #438, we've reduced the recommended age for mcribs to the first three months, and based on your MNIInfant cohort it looks like you are past that.

[dnkennedy]

Just to close this out. It was a process that was running, but on an older version of nibabies, and without using the "--derivatives smriprep..." directive. But, my error was unstable, I couldn't recreate it (generated other errors) and others could not recreate it (generated different errors). So we restarted our approach, with current nibabies version, at the actual HPC and using the singularity version, where we were going to run these for 'production' anyway, and now are not getting any error. So, I will close this as either version obsolete, or issues with my local Docker configuration, or something else completely.